Ming Chen
12/01/2017
Get Singularity ready on my local computer
mkdir -p ~/Desktop/singularity-images && cd ~/Desktop/singularity-images
docker run -it --rm --privileged -v ~/Desktop/singularity-images:/home/singularity-images mingchen0919/docker-singularity
Pull a container with R installed to my local computer.
cd /home/singularity-images
singularity build --writable r.img docker://r-baseRun the R container
# check the image file
ls
# run container interactively
singularity shell --writable r.imgTest that the R package plyr does not exist before we install it
R
require('plyr')Install package plyr
install.packages('plyr')
require('plyr')Exit the singularity container
exitTransfer the container to a HPC cluster
scp r.img mchen33@149.165.156.175:/home/mchen33/r.imgRun the container on the HPC cluster as non-root user.
# login to the HPC cluster
ssh mchen33@149.165.156.175
singularity shell r.img
# check the testing package
R
require('plyr')We are going to use the Docker container created by Björn Grüning.
Launch a docker container which has galaxy installed
docker run -it --rm --name=galaxy_instance \
-p 80:80 -p 8021:21 -p 8022:22 \
-e "ENABLE_TTS_INSTALL=True" \
-e "GALAXY_CONFIG_ADMIN_USERS=example@gmail.com" \
bgruening/galaxy-stable:17.01 /bin/bashStart Galaxy
startupSign up an account
example@gmail.com.
Install fastqc and trimmomatic
fastqc and select the one owned by devteam and installtrimmomatic and select the one owned by pjbriggs and install
Build and run Galaxy workflows
reads quality control workflow.fastqc and trimmomatic tools to the workflow creating panel and connect them to create workflows.Build workflow from history
Build your own Galaxy docker container
docker commit [CONTAINER ID] mingchen0919/my-galaxy
docker ps -a
docker push mingchen0919/my-galaxy
Having admin access to a running Galaxy instance.
Admin user API key
Link Tripal to Galaxy
Run Galaxy workflows from Tripal site
Galaxy Tool Generator (GTG) is a web-based platform for asisting Galaxy tool development. The components of the GTG platform includes:
Galaxy Tool Generator & Galaxy Tool Generator UIThe platform is still under development. The code below will eventually replaced by a one line command.
mkdir -p ~/Desktop/galaxy-tool-generator-dev && cd ~/Desktop/galaxy-tool-generator-dev
git clone https://github.com/MingChen0919/galaxy_tool_generator.git
git clone https://github.com/MingChen0919/galaxy_tool_generator_ui.git
git clone https://github.com/galaxyproject/blend4php.git
docker run -it -p 8090:80 --rm --network=galaxy_tool_generator_nw \
-v $(pwd)/galaxy_tools:/var/www/html/sites/default/files/galaxy_tools \
-v $(pwd)/galaxy_tool_generator:/var/www/html/sites/all/modules/galaxy_tool_generator \
-v $(pwd)/galaxy_tool_generator_ui:/var/www/html/sites/all/modules/galaxy_tool_generator_ui \
-v $(pwd)/blend4php:/var/www/html/sites/all/libraries/blend4php \
mingchen0919/docker-galaxy-tool-generator '/bin/bash'
drush en -y galaxy_tool_generator galaxy_tool_generator_uiGo to http://127.0.0.1:8090/
See https://testtoolshed.g2.bx.psu.edu/ and search for test_galaxy_tool_generator.
cd ~/Desktop/galaxy-tool-generator-dev && mkdir shed_tools
docker run -it --rm --network=galaxy_tool_generator_nw --name=galaxy_instance \
-p 8080:80 -p 8021:21 -p 8022:22 \
-v $(pwd)/shed_tools:/export/shed_tools \
-e "ENABLE_TTS_INSTALL=True" \
-e "GALAXY_CONFIG_ADMIN_USERS=example@gmail.com" \
bgruening/galaxy-stable:17.01 /bin/bashstartupRegister an account on Galaxy instance
Install a testing tool (e.g., the test_galaxy_tool_generator tool from test tool shed).
Simutaneously testing modified tools on Galaxy (under development)